On Fri, Aug 3, 2012 at 3:34 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 8/3/12 10:27 AM, Steven Neumann wrote: >> >> Dear Gmx Users, >> >> I want to simulate protein line chain (80 residues) in explicit >> sovent. Let's assume its axis is x direction. What should be the z and >> y dimension of the box? Is there any rule? Would you wait e.g. for 50 > > > The box size in all dimensions needs to be sufficient to accommodate the > protein chain in a fully extended configuration aligned with any axis. You > can't predict how the protein will rotate, and it is possible (though > probably unlikely) to rotate 90 degrees in any direction without collapsing > at all. A dodecahedral box is your friend here, but a huge amount of atoms > is unavoidable. > > >> ns when it folds and then decrease the simulation box? >> > > In doing so, you have to justify your results in the context of a > discontinuous series of simulations. Implicit solvent may be a much more > advantageous approach. > > -Justin
Thank you. What do you mean by discontinuous series of simulations? I have to use explicit solvent unfortunately. Once it folds in a huge box I can stop it and place it into the smaller one. Steven > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists